Matt Pahl retweeted
Integrated epigenetic and genetic programming of primary human T cells nature.com/articles/s41587-0…
Matt Pahl retweeted
Origins and implications of intron retention quantitative trait loci in human tissues by Eddie Park and Yi Xing at @ChildrensPhila
hubs.li/Q04zqZ4j0
@AJHGNews (@GeneticsSociety) highlight from the best of collection 2025-2026
Matt Pahl retweeted
What distinguishes successful from failed reprogramming to iPSC? In this new preprint, part of our @IGVFConsortium efforts, we used single cell methylation, Hi-C, RNA and ATAC, and spatial RNA to answer this question biorxiv.org/content/10.64898…
Matt Pahl retweeted
Come by our Round Table event at #SleepEurope2026!
"New approaches to identifying genes regulating sleep and/or conferring risk for sleep disorders".
Room 0.2, Thurs 8.30-9.30am
With @atothezphd , Allan Pack, @AlexCarlKeene and Jason Rihel.
Matt Pahl retweeted
Also, MACS3 paper is out, updating our 18yrs old reference paper after years of maintenance and development. Many thanks to the community for the continuous contributions and to CZI @cziscience EOSS program for the support. doi.org/10.1093/gpbjnl/qzag0… 2/2
Matt Pahl retweeted
Check out our new preprint led by @mileshuseyin unexpectedly discovering Polycomb 3D interactions independent of cPRC1.
Miles led this ambitious study. He's also on the faculty job market, and I can't recommend him highly enough for important and comprehensive science!
1/9) Excited to share my preprint on Polycomb 3D chromatin interactions from my postdoc with @Anders_S_Hansen!
We were surprised to find that canonical PRC1 doesn't seem to be the only contributor to these interactions:
biorxiv.org/content/10.64898…
Matt Pahl retweeted
Are weak TF motifs important? @ZeitlingerLab use deep learning to systematically map low-affinity pioneer binding sites in mESCs and show that they cooperate with strong motifs to open chromatin. Preview w/ @gracecbower: cell.com/cell-genomics/fullt… Paper: cell.com/cell-genomics/fullt…
Matt Pahl retweeted
Spatial isotope tracing maps compartmentalized nutrient use across the adult fruit fly
Moon, Huang, Blum, New, Park, Chen, Nishida, Pister, Nahid, Hu, Tennessen, Fraenkel, Asara, Davidson, Perrimon
doi: doi.org/10.64898/2026.10.06.…
Matt Pahl retweeted
Preprint from graduate student, @maweidekamp - NOW SEEKING A POSTDOC ROLE! Co-mentored with @bvoight28. Single-cell eQTL mapping in human pancreas. New signals not seen in bulk studies. Cell types of action implicated @CHOP_Research @PennGenetics
biorxiv.org/content/10.64898…
Matt Pahl retweeted
This paper from the Stark lab introduces BARe-seq, extending MPRAs by preserving the distribution of transcriptional output across individual plasmids rather than aggregating, allowing them to decompose mean expression into burst size and burst frequency.
biorxiv.org/content/10.64898…
Matt Pahl retweeted
Single-Cell Study Designs Are Systematically Underpowered for Small-Effect Genes.
biorxiv.org/content/10.64898…
Matt Pahl retweeted
Until now, inserting a gene size change into the genome only worked in dividing cells. Now, you can write a whole gene into a chosen spot in the genome of a cell that will never divide again (e.g., neurons, etc).
doi.org/10.1038/s41586-026-1…
Matt Pahl retweeted
Read our paper for the full story & discussion of how this fits with the work of others in the field. Also check out a recent paper by the Wysocka, @Anders_S_Hansen & @ABoettiger labs describing a phenomenon with many similarities in mammalian cells:
nature.com/articles/s41588-0…
Matt Pahl retweeted
Mechanisms underlying disease-causing variants in promoters and enhancers nature.com/articles/s41588-0…
Matt Pahl retweeted
I’m delighted to share our latest work on the 3D epigenome of glial cell types in the developing human cortex, published today in Nature!
rdcu.be/CPbL73mz3STa
Matt Pahl retweeted
Our genetic association study of the Big Five personality traits (extraversion, agreeableness, conscientiousness, neuroticism and openness to experience) came out in @Nature today, check it out here (open access): nature.com/articles/s41586-0…
Matt Pahl retweeted
RESEARCH PAPER: Machine learning analysis of the human initiator region reveals key features of different types of core promoters
By Rhyne-Carrigg et al., and James T. Kadonaga
➡️ genesdev.cshlp.org/content/4…
@UCSanDiego @ucsdbiosciences
#transcription #machinelearning
Matt Pahl retweeted
How often is autism caused by de novo changes to the genome? What is the spectrum of penetrance across autism-associated genes? What can we expect from future autism gene discovery? I'm pleased to share a new preprint where we develop new statistical methods to answer these Qs.
Matt Pahl retweeted
🆕 ADVANCE ONLINE 🆕
RESEARCH PAPER: Machine learning analysis of the human initiator region reveals key features of different types of core promoters
By Rhyne-Carrigg et al., and James Kadonaga
➡️ ow.ly/Fij250ZzqQP
@UCSanDiego @ucsdbiosciences
#transcription
Matt Pahl retweeted
New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee &
@CGBiar! Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n biorxiv.org/content/10.64898…
